Read Skyline exported files
read_skyline(files)Character vector with filepaths to Skyline exported files in CSV format.
LipidomicsExperiment object.
datadir <- system.file("extdata", package = "lipidr")
# all csv files
filelist <- list.files(datadir, "data.csv", full.names = TRUE)
d <- read_skyline(filelist)
#> Successfully read 3 methods.
#> Your data contain 58 samples, 10 lipid classes, 277 lipid molecules.
# View automatically generated lipid annotations
rowData(d)
#> DataFrame with 279 rows and 26 columns
#> filename Molecule Precursor.Mz Precursor.Charge Product.Mz
#> <character> <character> <numeric> <integer> <numeric>
#> 1 A1_data.csv PE 32:0 692.5 1 551.5
#> 2 A1_data.csv PE 32:1 690.5 1 549.5
#> 3 A1_data.csv PE 32:2 688.5 1 547.5
#> 4 A1_data.csv PE 34:1 718.5 1 577.5
#> 5 A1_data.csv PE 34:1 NEG 716.5 1 196.0
#> ... ... ... ... ... ...
#> 275 F2_data.csv PC(P-40:3) 824.600 1 184.10
#> 276 F2_data.csv PC(P-40:4) 822.600 1 184.10
#> 277 F2_data.csv PC(P-40:5) 820.600 1 184.10
#> 278 F2_data.csv PC(P-40:6) 818.600 1 184.10
#> 279 F2_data.csv 15:0-18:1(d7) PC 753.615 1 184.07
#> Product.Charge clean_name ambig not_matched istd class_stub
#> <integer> <factor> <logical> <logical> <logical> <character>
#> 1 1 PE 32:0 FALSE FALSE FALSE PE
#> 2 1 PE 32:1 FALSE FALSE FALSE PE
#> 3 1 PE 32:2 FALSE FALSE FALSE PE
#> 4 1 PE 34:1 FALSE FALSE FALSE PE
#> 5 1 PE 34:1 FALSE FALSE FALSE PE
#> ... ... ... ... ... ... ...
#> 275 1 PCP-40:3 FALSE FALSE FALSE PCP
#> 276 1 PCP-40:4 FALSE FALSE FALSE PCP
#> 277 1 PCP-40:5 FALSE FALSE FALSE PCP
#> 278 1 PCP-40:6 FALSE FALSE FALSE PCP
#> 279 1 PC 15:0-18:1(d7) FALSE FALSE TRUE PC
#> chain1 l_1 s_1 chain2 l_2 s_2 chain3
#> <character> <integer> <integer> <character> <integer> <integer> <character>
#> 1 32:0 32 0 NA NA
#> 2 32:1 32 1 NA NA
#> 3 32:2 32 2 NA NA
#> 4 34:1 34 1 NA NA
#> 5 34:1 34 1 NA NA
#> ... ... ... ... ... ... ... ...
#> 275 40:3 40 3 NA NA
#> 276 40:4 40 4 NA NA
#> 277 40:5 40 5 NA NA
#> 278 40:6 40 6 NA NA
#> 279 15:0 15 0 18:1 18 1
#> l_3 s_3 chain4 l_4 s_4 total_cl total_cs
#> <logical> <logical> <character> <logical> <logical> <integer> <integer>
#> 1 NA NA NA NA 32 0
#> 2 NA NA NA NA 32 1
#> 3 NA NA NA NA 32 2
#> 4 NA NA NA NA 34 1
#> 5 NA NA NA NA 34 1
#> ... ... ... ... ... ... ... ...
#> 275 NA NA NA NA 40 3
#> 276 NA NA NA NA 40 4
#> 277 NA NA NA NA 40 5
#> 278 NA NA NA NA 40 6
#> 279 NA NA NA NA 33 1
#> Class
#> <character>
#> 1 PE
#> 2 PE
#> 3 PE
#> 4 PE
#> 5 PE
#> ... ...
#> 275 PC
#> 276 PC
#> 277 PC
#> 278 PC
#> 279 PC